As a part of molecular taxonomic revision of the bloom-forming blue-green alga Microcystis, allozyme divergence of the Japanese strains of Microcystis were studied with special reference to their morphology and toxicity. We analyzed (1) allozyme genotype at four enzyme loci, IDH, 6PGD, PGI and PGM, (2) average cell size and characteristics of colony morphology and (3) toxin composition of three microcystins (-RR, -YR, -LR), using a total of 78 strains collected from twenty-three lakes, ponds and reservoirs. As a result of statistical analyses of allozyme genotype, it was elucidated that the genus Microcystis consists of at least five taxonomic entities listed below. Morphological and biochemical attributes of the five taxonomic entities are summarized as follows.(1) M. aeruginosa S1-type : cell size small, colony not characteristic, untoxic.(2) M. aeruginosa S2-type : cell size small, colony not characteristic, toxic.(3) M. aeruginosa L-type : cell size large, clathrate colony, highly toxic.(4) M. viridis : cell size large, cubic colony, toxic.(5) M. wesenbergil : cell size large, pouched colony, nontoxic.These achievements will provide a new taxonomic system and identification method (including forecast of toxicity) of the genus Microcystis.